Analysis of Forensic SNPs in the Canine mtDNA HV1 Mutational Hotspot Region*

Baute, Danielle T.; Satkoski, Jessica; Spear, Theresa F.; Smith, David Glenn; Dayton, Melody; Malladi, Venkat S.; Goyal, B S Vivek; Kou, B S Alexander; Kinaga, L B S Jennifer; Kanthaswamy, Sreetharan

doi:10.1111/j.1556-4029.2008.00880.x

Cited by 18 publications

(17 citation statements)

References 12 publications

(44 reference statements)

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“…(36) and Baute et al. (37) that were based on canine mitochondrial DNA (mtDNA). As such, in forensic casework, estimates of genetic diversity based on regional populations proximate to the crime scene may also exhibit a similar genetic structure represented by samples collected from different and diverse geographic regions.…”

Section: Discussionmentioning

confidence: 99%

Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework*

Kanthaswamy

Tom

Mattila³

et al. 2009

Journal of Forensic Sciences

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Canine biological specimens are often part of the physical evidence from crime scenes. Until now, there have been no validated canine-specific forensic reagent kits available. A multiplex genotyping system, comprising 18 short tandem repeats (STRs) and a sex-linked zinc finger locus for gender determination, was developed for generating population genetic data assessing the weight of canine forensic DNA profiles. Allele frequencies were estimated for 236 pedigreed and 431 mixed breed dogs residing in the U.S. Average random match probability is 1 in 2 x 10(33) using the regional database and 1 in 4 x 10(39) using the breed dataset. Each pedigreed population was genetically distinct and could be differentiated from the mixed breed dog population but genetic variation was not significantly correlated with geographic transition. Results herein support the use of the allele frequency data with the canine STR multiplex for conveying the significance of identity testing for forensic casework, parentage testing, and breed assignments.

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Section: Discussionmentioning

confidence: 99%

Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework*

Kanthaswamy

Tom

Mattila³

et al. 2009

Journal of Forensic Sciences

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“…As a result, even if there are many rare haplotypes, the discriminatory power of the dog mtDNA control region is limited (Savolainen et al 1997, Wetton et al 2003, Angleby and Savolainen 2005, Halverson and Basten 2005, Eichmann and Parson 2007, Gundry et al 2007, Baute et al 2008, Hassell et al 2008, Himmelberger et al 2008, Desmyter and Comblez 2009, Webb and Allard 2009a, Smalling et al 2010, Desmyter and Gijsbers 2012, Imes et al 2012). This is well illustrated by comparing the mtDNA characteristics of nine forensic population studies which all consider at least positions 15458 to 16030 in HV-I.…”

Section: Estimating Population Frequencies Of Dog Mtdna Haplotypes Fomentioning

confidence: 99%

Reviewing population studies for forensic purposes: Dog mitochondrial DNA

Verscheure¹,

Backeljau²,

Desmyter³

2013

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The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.

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“…Mitochondrial DNA (mtDNA) has been demonstrated to be a valuable tool for genetic characterization of animal samples [1–3]. Many studies had been implemented focusing on these DNA sequences to evaluate the genetic diversity of dog populations [4, 5], determine the evolution relationship among them [6], or trace the origin of a dog breed [7–9].…”

Section: Introductionmentioning

confidence: 99%

“…Annotated haplotype information can be deduced from a small region (60 bp) [3], from the 582 bp region [11], from the 660 bp region [18] in the mtDNA HV1, or from the combination of the 582 bp region and the mtDNA HV2 [19]… in which, the 582 bp region was used in most recent studies [9, 11, 20–22]. According to this system, all haplotypes of dog mtDNA belongs to six phylogenetic groups named from A to F. A haplotype was named by the corresponding haplogroup followed by an Arabic numeral (e.g., B15) [20].…”

Section: Introductionmentioning

confidence: 99%

Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database

2017

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BackgroundCanine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes.DescriptionThe Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD.The CHD can be accessed at http://chd.vnbiology.com. It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download.ConclusionsThe Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0528-0) contains supplementary material, which is available to authorized users.

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Analysis of Forensic SNPs in the Canine mtDNA HV1 Mutational Hotspot Region*

Cited by 18 publications

References 12 publications

Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework*

Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework*

Reviewing population studies for forensic purposes: Dog mitochondrial DNA

Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database

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